/// <summary> /// Get the alignment results /// </summary> /// <param name="serviceParameters">job id, control id</param> /// <returns>alignment</returns> public ClustalWResult FetchResultsAsync(ServiceParameters serviceParameters) { string output = _baseClient.GetOutputAsString(serviceParameters.JobId, serviceParameters.Parameters[CONTROLID].ToString()); IList <ISequenceAlignment> alignments = _ClustalWParser.Parse(new StringReader(output)); return(new ClustalWResult(alignments[0])); }
/// <summary> /// Get the alignment results /// </summary> /// <param name="serviceParameters">job id, control id</param> /// <returns>alignment</returns> public ClustalWResult FetchResultsAsync(ServiceParameters serviceParameters) { IList <ISequenceAlignment> alignments = null; if (null == serviceParameters) { throw new ArgumentNullException("Parameters"); } string output = _baseClient.GetOutputAsString(serviceParameters.JobId, serviceParameters.Parameters[CONTROLID].ToString()); using (StringReader reader = new StringReader(output)) { alignments = _ClustalWParser.Parse(reader); } return(new ClustalWResult(alignments[0])); }
/// <summary> /// Parses the sequences from the given filename. /// </summary> /// <param name="parser">Sequence Parser</param> /// <param name="fileName">Filename to open/close</param> /// <returns>Set of parsed sequences.</returns> public static IEnumerable <ISequenceAlignment> Parse(this ISequenceAlignmentParser parser, string fileName) { using (FileStream fs = File.OpenRead(fileName)) { foreach (var item in parser.Parse(fs)) { yield return(item); } } }
/// <summary> /// Parses the sequences from the open file. /// </summary> /// <param name="parser">Sequence Parser</param> /// <returns>Set of parsed sequences.</returns> public static IEnumerable <ISequenceAlignment> Parse(this ISequenceAlignmentParser parser) { var fs = ParserFormatterExtensions <ISequenceAlignmentParser> .GetOpenStream(parser, false); if (fs == null) { throw new Exception("You must open a parser before calling Parse."); } return(parser.Parse(fs)); }
public void ValidateSamParserWithDVIscFile() { // Gets the expected sequence from the Xml string filePath = _utilityObj._xmlUtil.GetTextValue( Constants.SAMFileWithRefNode, Constants.FilePathNode); ISequenceAlignmentParser iSeqParser = SequenceAlignmentParsers.FindParserByFile(filePath); if (null != iSeqParser) { IVirtualSequenceAlignmentParser vParserObj = iSeqParser as IVirtualSequenceAlignmentParser; if (null != vParserObj) { vParserObj.EnforceDataVirtualization = true; } else { Assert.Fail("SAM P1 Cases : Could not find the SAM Parser Object."); } string iscFilePath = string.Concat(filePath, ".isc"); iSeqParser.Parse(filePath); if (File.Exists(iscFilePath)) { Console.WriteLine( "SAM P1 Cases : DV enabled as expected and isc file created successfully."); ApplicationLog.WriteLine( "SAM P1 Cases : DV enabled as expected and isc file created successfully."); } else { Assert.Fail("SAM P1 Cases : DV not enabled as expected."); } } else { Assert.Fail("SAM P1 Cases : Could not find the SAM file"); } }